Don't feel badly about this. Humans by nature are gullible, just look around to any consumer marketplace or beliefe systems.
In essence, you are saying that there is no difference in sound quality, using the digital out, between a budget and high-end CD player. Wow! I can scarcely believe it!
Yep, that is correct. How could the digital signal be altered to alter the analog signal conversion? The digital signal on a CD is grouped and scrambled, in easy to follow language

(Reed Solomon cross interleaving, I believe it to be). To alter it, youy'd have to know which portions, where it is in the scrambled eggs to alter it intelligently, such as altering the high frequencies only.
You read my mind!
But I am not Sylvia Brown
After reading further Audioholics papers, I have been giving some thought to purchasing the Radio Shack (analogue) SPL meter in addition to AVIAs Guide to home theatre.
This is a small investment to add to your audio tool kit. The Avia has the video feature to adjust each color intensity, not sure if that Digital has it but, even adding that as a second test disc is a cheap investment and would recommend that too. Certainly cheaper than expensive wire of players and more productive results
1. Is it recommended that I also purchase JKPs Digital video essentials for use with my DLP projector, or will AVIAs DVD do?
As above, I would. Not that expensive. Look around for it. Amazon may have it available in used DVD, cheap. Make sure it has all the filters with it for the video tune up.
2. The following is a quote from the Audioholics paper Subwoofer Calibration Using Rives Audio Test CD 2: "Also, I had to increase the amount of delay to 20 feet even though the subwoofer is only 13 feet away." Doesn't this mean that the timing of the LFE information would be incorrect? Or does this not matter due to the non-directional nature of the sub coupled with the speed of sound and the 20-13=7 feet distance?
I read that too but not sure what to make of it. You may want to ask that in a new thread but tune yours to the classic setup, measure with tape and use that.
3. Armed with a tape measure, SPL meter, and my own limited knowledge, I have enough self-confidence (/over-confidence?!!) to manually set the wiring, distance, size and level parameters.
Go for it. All it can do is not sound quite right but it won'd harm any component.
However, this still leaves the Equalizing (composed of Frequency, level and Q-factor) which YPAO automatic calibration sets. Is it ill-advised to tamper with these? If not, where can I read-up on these subjects?
Try the auto setup and see what distances it comes up with. If it is close, leave it. If far off, I'd change to what you measures but the EQ will be set well enough. You can also ask this in a new thread.
Finally, thanks for your replies. I am discovering that it can sometimes be quite tricky to post replies; most especially opinions, without conveying the feeling of 'stepping on someones toes'!
Hey, don't feel like the Lone Ranger

You will get the hang of it and stepping on toes are why we are here.

Besides, no one will phisically strike back, I hope. Part of learning, asking and part of life.